Thu Nov 21 02:20:32 UTC 2024 I: starting to build ncbi-seg/trixie/i386 on jenkins on '2024-11-21 02:20' Thu Nov 21 02:20:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_14/51515/console.log Thu Nov 21 02:20:32 UTC 2024 I: Downloading source for trixie/ncbi-seg=0.0.20000620-7 --2024-11-21 02:20:32-- http://deb.debian.org/debian/pool/main/n/ncbi-seg/ncbi-seg_0.0.20000620-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2214 (2.2K) [text/prs.lines.tag] Saving to: ‘ncbi-seg_0.0.20000620-7.dsc’ 0K .. 100% 235M=0s 2024-11-21 02:20:32 (235 MB/s) - ‘ncbi-seg_0.0.20000620-7.dsc’ saved [2214/2214] Thu Nov 21 02:20:32 UTC 2024 I: ncbi-seg_0.0.20000620-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ncbi-seg Binary: ncbi-seg Architecture: any Version: 0.0.20000620-7 Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille , Pranav Ballaney Homepage: https://ftp.ncbi.nih.gov/pub/seg/seg/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-seg Vcs-Git: https://salsa.debian.org/med-team/ncbi-seg.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: ncbi-seg deb science optional arch=any Checksums-Sha1: 77e02bb00844c2486a568ae8dcbecdcb537ccee5 86796 ncbi-seg_0.0.20000620.orig.tar.gz abd512c45a425619e16b28a4614f2513c90b70f0 11736 ncbi-seg_0.0.20000620-7.debian.tar.xz Checksums-Sha256: 77f5e92dd2f70ff70459c412a503d32a33f034c52c678ce152cf03149ae293e4 86796 ncbi-seg_0.0.20000620.orig.tar.gz b05aee643b9bbc0c654ff0fbf3113adfa89ecf9a979f5c0458726f96c47059a5 11736 ncbi-seg_0.0.20000620-7.debian.tar.xz Files: 97b66e1c72c6894be7559a72fdcdde7b 86796 ncbi-seg_0.0.20000620.orig.tar.gz ddb90b09f09551ab71526cee9f7cac28 11736 ncbi-seg_0.0.20000620-7.debian.tar.xz Dgit: 2ce23cce57e17a2838b3fafd564d6242e1a354c8 debian archive/debian/0.0.20000620-7 https://git.dgit.debian.org/ncbi-seg -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbUs1IUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrnxBAAsjLC3/LR2CoNy6PYhWre7dvQQTJ0 wCDNelaXInuQOlNcgs2HGLdrJ3jqQ3V4zD05AcsABZHRXNxpVBQfYW70SZetvlWv MeVvuaUMjlimyvMv/dzI0oRfnK1qjA2K2w02ZEjlXjNzSONj4gRKKanoUtmefSC0 8dKfCRUBegCBN5l1k8IETrvts2W+hhgEkujPgkkStv+JIK8gh+mVIJ7R6wAJ6q3y W9EfERRAVppOx06fn7GpWgE1GRXl/8cluBAkMCu4gbOdifqv8LuikVcG6bLq/Ym/ GHpxOQI3PyHvkSF+XPDjBfGVZwEjcI/dndLof+kF4jCM6y8bGFHzPfwJO2xXMVVG 7bbcJN+9QintnAfMkQDXtxMIZ2yV1D2eoRXFwm1tdSEdbtR5XC2DPv3/RJvMKx4Y ezrxBiAuUH84ZhJxtaCxw82kby7iG0kC9lomQZ2BFOWFDgl3BZZYixJa3FgBb62u Q+8dlnXyfqop79EIuGzpiFOGrxYdudU0FbH+aAXdDQX+g+Ue4LoKSiuTYU/bROL2 RTMYizNos+SK75XPBCTSO+qdPdCXd4XB0hBQ7jwpSPXw9B/UCiM1ZRrUETSx8HlI VLhQitVAxHZudOFQ+YcGNC8h2c5zjQIPist6S9yQ5t0ns8mOQ/o8TIjoYPJiBv/7 aGhlA34RUmTShzI= =cEfP -----END PGP SIGNATURE----- Thu Nov 21 02:20:32 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 02:20:32 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Thu Nov 21 02:20:32 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Thu Nov 21 02:20:56 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 23 20:43:34 -12 2025 I: pbuilder-time-stamp: 1766565814 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [ncbi-seg_0.0.20000620-7.dsc] I: copying [./ncbi-seg_0.0.20000620.orig.tar.gz] I: copying [./ncbi-seg_0.0.20000620-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Sep 1 18:32:50 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ncbi-seg_0.0.20000620-7.dsc: no acceptable signature found dpkg-source: info: extracting ncbi-seg in ncbi-seg-0.0.20000620 dpkg-source: info: unpacking ncbi-seg_0.0.20000620.orig.tar.gz dpkg-source: info: unpacking ncbi-seg_0.0.20000620-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile dpkg-source: info: applying example dpkg-source: info: applying seg.c dpkg-source: info: applying genwin.c dpkg-source: info: applying autotools dpkg-source: info: applying seg.pod dpkg-source: info: applying clang.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7608/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5b6742f1001f47ba9d109f1a3de81da0' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7608' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/pbuilderrc_y6kJ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/b1 --logfile b1/build.log ncbi-seg_0.0.20000620-7.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7608/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After unpacking 75.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Fetched 20.1 MB in 1s (34.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../21-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../23-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ncbi-seg-0.0.20000620/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ncbi-seg_0.0.20000620-7_source.changes dpkg-buildpackage: info: source package ncbi-seg dpkg-buildpackage: info: source version 0.0.20000620-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/ncbi-seg-0.0.20000620' dh_autoreconf -X./COPYING configure.ac:5: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' Makefile.am: installing './INSTALL' Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/reproducible-path/ncbi-seg-0.0.20000620' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands dh_auto_build make -j6 make[1]: Entering directory '/build/reproducible-path/ncbi-seg-0.0.20000620' gcc -DPACKAGE_NAME=\"ncbi-seg\" -DPACKAGE_TARNAME=\"ncbi-seg\" -DPACKAGE_VERSION=\"0.0.20000620\" -DPACKAGE_STRING=\"ncbi-seg\ 0.0.20000620\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ncbi-seg\" -DVERSION=\"0.0.20000620\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ncbi-seg-0.0.20000620=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=implicit-function-declaration -Wno-error=implicit-int -c -o seg.o seg.c gcc -DPACKAGE_NAME=\"ncbi-seg\" -DPACKAGE_TARNAME=\"ncbi-seg\" -DPACKAGE_VERSION=\"0.0.20000620\" -DPACKAGE_STRING=\"ncbi-seg\ 0.0.20000620\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ncbi-seg\" -DVERSION=\"0.0.20000620\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ncbi-seg-0.0.20000620=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=implicit-function-declaration -Wno-error=implicit-int -c -o genwin.o genwin.c sed -e 's|__datadir__|/usr/share|g;s|__docdir__|/usr/share/doc/ncbi-seg|g;s|__pkgdatadir__|/usr/share/ncbi-seg|g;s|__PREFIX__|/usr|g;s|__sysconfdir__|/etc|g;s|__VERSION__|0.0.20000620|g;' "ncbi-seg.pod" | \ pod2man -c 'User Commands' -r "0.0.20000620" -name NCBI-SEG > "ncbi-seg.1" In file included from genwin.c:9: genwin.h:146:8: warning: type defaults to 'int' in declaration of 'closedbase' [-Wimplicit-int] 146 | extern closedbase(); | ^~~~~~~~~~ genwin.h:149:8: warning: type defaults to 'int' in declaration of 'closeseq' [-Wimplicit-int] 149 | extern closeseq(); | ^~~~~~~~ genwin.h:152:8: warning: type defaults to 'int' in declaration of 'shiftwin' [-Wimplicit-int] 152 | extern shiftwin(), closewin(); | ^~~~~~~~ genwin.h:152:20: warning: type defaults to 'int' in declaration of 'closewin' [-Wimplicit-int] 152 | extern shiftwin(), closewin(); | ^~~~~~~~ genwin.h:154:8: warning: type defaults to 'int' in declaration of 'compon' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~~ genwin.h:154:18: warning: type defaults to 'int' in declaration of 'stateon' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~~~ genwin.h:154:29: warning: type defaults to 'int' in declaration of 'enton' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~ genwin.h:158:8: warning: type defaults to 'int' in declaration of 'closemat' [-Wimplicit-int] 158 | extern closemat(); | ^~~~~~~~ genwin.h:160:8: warning: type defaults to 'int' in declaration of 'upper' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~ genwin.h:160:17: warning: type defaults to 'int' in declaration of 'lower' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~ genwin.h:160:26: warning: type defaults to 'int' in declaration of 'findchar' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~~~~ genwin.c:62:1: warning: return type defaults to 'int' [-Wimplicit-int] 62 | genwininit() | ^~~~~~~~~~ In file included from seg.c:10: genwin.h:146:8: warning: type defaults to 'int' in declaration of 'closedbase' [-Wimplicit-int] 146 | extern closedbase(); | ^~~~~~~~~~ genwin.h:149:8: warning: type defaults to 'int' in declaration of 'closeseq' [-Wimplicit-int] 149 | extern closeseq(); | ^~~~~~~~ genwin.h:152:8: warning: type defaults to 'int' in declaration of 'shiftwin' [-Wimplicit-int] 152 | extern shiftwin(), closewin(); | ^~~~~~~~ genwin.h:152:20: warning: type defaults to 'int' in declaration of 'closewin' [-Wimplicit-int] 152 | extern shiftwin(), closewin(); | ^~~~~~~~ genwin.h:154:8: warning: type defaults to 'int' in declaration of 'compon' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~~ genwin.h:154:18: warning: type defaults to 'int' in declaration of 'stateon' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~~~ genwin.h:154:29: warning: type defaults to 'int' in declaration of 'enton' [-Wimplicit-int] 154 | extern compon(), stateon(), enton(); | ^~~~~ genwin.h:158:8: warning: type defaults to 'int' in declaration of 'closemat' [-Wimplicit-int] 158 | extern closemat(); | ^~~~~~~~ genwin.h:160:8: warning: type defaults to 'int' in declaration of 'upper' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~ genwin.h:160:17: warning: type defaults to 'int' in declaration of 'lower' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~ genwin.h:160:26: warning: type defaults to 'int' in declaration of 'findchar' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~~~~ genwin.c: In function 'opendbase': genwin.c:93:8: warning: implicit declaration of function 'blastdb' [-Wimplicit-function-declaration] 93 | if (blastdb(name)) | ^~~~~~~ genwin.c: At top level: genwin.c:144:8: warning: return type defaults to 'int' [-Wimplicit-int] 144 | extern closedbase(dbase) | ^~~~~~~~~~ genwin.c:185:8: warning: return type defaults to 'int' [-Wimplicit-int] 185 | extern closeseq(seq) | ^~~~~~~~ genwin.c:319:8: warning: return type defaults to 'int' [-Wimplicit-int] 319 | extern closewin(win) | ^~~~~~~~ genwin.c:336:8: warning: return type defaults to 'int' [-Wimplicit-int] 336 | extern compon(win) | ^~~~~~ genwin.c:364:8: warning: return type defaults to 'int' [-Wimplicit-int] 364 | extern stateon(win) | ^~~~~~~ genwin.c:389:8: warning: return type defaults to 'int' [-Wimplicit-int] 389 | extern enton(win) | ^~~~~ genwin.c: In function 'readentry': genwin.c:510:9: warning: implicit declaration of function 'readhdr' [-Wimplicit-function-declaration] 510 | if (!readhdr(seq)) | ^~~~~~~ genwin.c:528:4: warning: implicit declaration of function 'readseq' [-Wimplicit-function-declaration] 528 | readseq(seq); | ^~~~~~~ genwin.c: At top level: genwin.c:545:1: warning: return type defaults to 'int' [-Wimplicit-int] 545 | readhdr(seq) | ^~~~~~~ genwin.c: In function 'readhdr': genwin.c:670:10: warning: implicit declaration of function 'skipline' [-Wimplicit-function-declaration] 670 | skipline(fp); | ^~~~~~~~ genwin.c: At top level: genwin.c:684:1: warning: return type defaults to 'int' [-Wimplicit-int] 684 | skipline(fp) | ^~~~~~~~ genwin.c:718:1: warning: return type defaults to 'int' [-Wimplicit-int] 718 | readseq(seq) | ^~~~~~~ genwin.c:794:8: warning: return type defaults to 'int' [-Wimplicit-int] 794 | extern upper(string, len) | ^~~~~ genwin.c:807:8: warning: return type defaults to 'int' [-Wimplicit-int] 807 | extern lower(string, len) | ^~~~~ genwin.c:862:1: warning: return type defaults to 'int' [-Wimplicit-int] 862 | tfree(ptr) | ^~~~~ seg.c:49:1: warning: return type defaults to 'int' [-Wimplicit-int] 49 | main(argc, argv) | ^~~~ seg.c: In function 'main': seg.c:58:4: warning: implicit declaration of function 'genwininit' [-Wimplicit-function-declaration] 58 | genwininit(); | ^~~~~~~~~~ seg.c:60:4: warning: implicit declaration of function 'getparams' [-Wimplicit-function-declaration] 60 | getparams(argc, argv); | ^~~~~~~~~ seg.c:61:4: warning: implicit declaration of function 'entropy_init' [-Wimplicit-function-declaration] 61 | entropy_init(window); | ^~~~~~~~~~~~ seg.c:72:7: warning: implicit declaration of function 'segseq' [-Wimplicit-function-declaration] 72 | segseq(seq, &segs, 0); | ^~~~~~ seg.c:73:7: warning: implicit declaration of function 'mergesegs' [-Wimplicit-function-declaration] 73 | mergesegs(seq, segs); | ^~~~~~~~~ seg.c:75:22: warning: implicit declaration of function 'singreport' [-Wimplicit-function-declaration] 75 | if (singleseq) singreport(seq, segs); | ^~~~~~~~~~ seg.c:76:27: warning: implicit declaration of function 'prettyreport' [-Wimplicit-function-declaration] 76 | else if (prettyseq) prettyreport(seq, segs); | ^~~~~~~~~~~~ seg.c:77:28: warning: implicit declaration of function 'pretreereport' [-Wimplicit-function-declaration] 77 | else if (prettytree) pretreereport(seq, segs); | ^~~~~~~~~~~~~ seg.c:78:12: warning: implicit declaration of function 'report' [-Wimplicit-function-declaration] 78 | else report(seq, segs); | ^~~~~~ seg.c:80:7: warning: implicit declaration of function 'freesegs' [-Wimplicit-function-declaration] 80 | freesegs(segs); | ^~~~~~~~ seg.c: At top level: seg.c:90:1: warning: return type defaults to 'int' [-Wimplicit-int] 90 | getparams(argc, argv) | ^~~~~~~~~ seg.c: In function 'getparams': seg.c:103:7: warning: implicit declaration of function 'usage' [-Wimplicit-function-declaration] 103 | usage(); | ^~~~~ seg.c:137:14: warning: implicit declaration of function 'getopt'; did you mean 'getsubopt'? [-Wimplicit-function-declaration] 137 | while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1) | ^~~~~~ | getsubopt seg.c: At top level: seg.c:210:1: warning: return type defaults to 'int' [-Wimplicit-int] 210 | segseq(seq, segs, offset) | ^~~~~~ seg.c: In function 'segseq': seg.c:233:16: warning: implicit declaration of function 'findlo' [-Wimplicit-function-declaration] 233 | loi = findlo(i, lowlim, H); | ^~~~~~ seg.c:234:16: warning: implicit declaration of function 'findhi'; did you mean 'findchar'? [-Wimplicit-function-declaration] 234 | hii = findhi(i, last, H); | ^~~~~~ | findchar seg.c:239:10: warning: implicit declaration of function 'trim' [-Wimplicit-function-declaration] 239 | trim(openwin(seq, leftend, rightend-leftend+1), &leftend, &rightend); | ^~~~ seg.c:252:21: warning: implicit declaration of function 'appendseg' [-Wimplicit-function-declaration] 252 | else appendseg(*segs, leftsegs); | ^~~~~~~~~ seg.c:273:14: warning: implicit declaration of function 'min'; did you mean 'main'? [-Wimplicit-function-declaration] 273 | i = min(hii, rightend+downset); | ^~~ | main seg.c: In function 'seqent': seg.c:312:31: warning: implicit declaration of function 'hasdash' [-Wimplicit-function-declaration] 312 | if (seq->punctuation && hasdash(win)) | ^~~~~~~ seg.c:314:10: warning: implicit declaration of function 'shiftwin1'; did you mean 'shiftwin'? [-Wimplicit-function-declaration] 314 | shiftwin1(win); | ^~~~~~~~~ | shiftwin seg.c: At top level: seg.c:326:1: warning: return type defaults to 'int' [-Wimplicit-int] 326 | hasdash(win) | ^~~~~~~ seg.c:343:1: warning: return type defaults to 'int' [-Wimplicit-int] 343 | findlo(i, limit, H) | ^~~~~~ seg.c:360:1: warning: return type defaults to 'int' [-Wimplicit-int] 360 | findhi(i, limit, H) | ^~~~~~ seg.c:377:1: warning: return type defaults to 'int' [-Wimplicit-int] 377 | trim(seq, leftend, rightend) | ^~~~ seg.c:507:1: warning: return type defaults to 'int' [-Wimplicit-int] 507 | mergesegs(seq, segs) | ^~~~~~~~~ seg.c:553:1: warning: return type defaults to 'int' [-Wimplicit-int] 553 | report(seq, segs) | ^~~~~~ seg.c: In function 'report': seg.c:565:7: warning: implicit declaration of function 'seqout'; did you mean 'seqent'? [-Wimplicit-function-declaration] 565 | seqout(seq, hi, 1, seq->length); | ^~~~~~ | seqent seg.c: At top level: seg.c:626:1: warning: return type defaults to 'int' [-Wimplicit-int] 626 | singreport(seq, segs) | ^~~~~~~~~~ seg.c:663:1: warning: return type defaults to 'int' [-Wimplicit-int] 663 | prettyreport(seq, segs) | ^~~~~~~~~~~~ seg.c: In function 'prettyreport': seg.c:687:9: warning: implicit declaration of function 'space'; did you mean 'isspace'? [-Wimplicit-function-declaration] 687 | space(leftspace+1); | ^~~~~ | isspace seg.c: At top level: seg.c:718:1: warning: return type defaults to 'int' [-Wimplicit-int] 718 | pretreereport(seq, segs) | ^~~~~~~~~~~~~ seg.c:811:1: warning: return type defaults to 'int' [-Wimplicit-int] 811 | space(len) | ^~~~~ seg.c:832:1: warning: return type defaults to 'int' [-Wimplicit-int] 832 | seqout(seq, hilo, begin, end) | ^~~~~~ seg.c:906:1: warning: return type defaults to 'int' [-Wimplicit-int] 906 | appendseg(segs, seg) | ^~~~~~~~~ seg.c:930:1: warning: return type defaults to 'int' [-Wimplicit-int] 930 | freesegs(segs) | ^~~~~~~~ seg.c:945:1: warning: return type defaults to 'int' [-Wimplicit-int] 945 | usage() | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ncbi-seg-0.0.20000620=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wl,-z,relro -Wl,-z,now -o ncbi-seg seg.o genwin.o -lm make[1]: Leaving directory '/build/reproducible-path/ncbi-seg-0.0.20000620' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/ncbi-seg/ make -j6 install DESTDIR=/build/reproducible-path/ncbi-seg-0.0.20000620/debian/ncbi-seg AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/ncbi-seg-0.0.20000620' make[2]: Entering directory '/build/reproducible-path/ncbi-seg-0.0.20000620' /usr/bin/mkdir -p '/build/reproducible-path/ncbi-seg-0.0.20000620/debian/ncbi-seg/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/ncbi-seg-0.0.20000620/debian/ncbi-seg/usr/share/man/man1' /usr/bin/install -c ncbi-seg '/build/reproducible-path/ncbi-seg-0.0.20000620/debian/ncbi-seg/usr/bin' /usr/bin/install -c -m 644 ncbi-seg.1 '/build/reproducible-path/ncbi-seg-0.0.20000620/debian/ncbi-seg/usr/share/man/man1' make[2]: Leaving directory '/build/reproducible-path/ncbi-seg-0.0.20000620' make[1]: Leaving directory '/build/reproducible-path/ncbi-seg-0.0.20000620' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'ncbi-seg' in '../ncbi-seg_0.0.20000620-7_i386.deb'. dpkg-deb: building package 'ncbi-seg-dbgsym' in '../ncbi-seg-dbgsym_0.0.20000620-7_i386.deb'. dpkg-genbuildinfo --build=binary -O../ncbi-seg_0.0.20000620-7_i386.buildinfo dpkg-genchanges --build=binary -O../ncbi-seg_0.0.20000620-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7608 and its subdirectories I: Current time: Tue Dec 23 20:43:55 -12 2025 I: pbuilder-time-stamp: 1766565835 Thu Nov 21 02:20:57 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Thu Nov 21 02:20:57 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Thu Nov 21 02:21:30 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Thu Nov 21 02:21:31 UTC 2024 I: ncbi-seg_0.0.20000620-7_i386.changes: Format: 1.8 Date: Sun, 01 Sep 2024 20:11:32 +0200 Source: ncbi-seg Binary: ncbi-seg ncbi-seg-dbgsym Architecture: i386 Version: 0.0.20000620-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: ncbi-seg - tool to mask segments of low compositional complexity in amino ac Closes: 1066563 Changes: ncbi-seg (0.0.20000620-7) unstable; urgency=medium . * Team upload. * d/rules: workaround build failure with gcc-14. (Closes: #1066563) * d/{control,copyright}: update homepage from ftp to https. * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: f987b7f381dfbd7c4b01e55434b428f03e6d0b20 26600 ncbi-seg-dbgsym_0.0.20000620-7_i386.deb 5dae91ac5bc8dcc481e66e126c18a10e3924dd1a 4951 ncbi-seg_0.0.20000620-7_i386.buildinfo c8ff927472475041603fa6a8fba2a566285b17fa 84464 ncbi-seg_0.0.20000620-7_i386.deb Checksums-Sha256: 87c3d55526d9b7cde14e203723110252e0d7511ca11a13480c0cc10f7d52a82d 26600 ncbi-seg-dbgsym_0.0.20000620-7_i386.deb 9a07a787b042398eb640dd5fb99f525ca2b81dc3b970854d009e7e11aeff4513 4951 ncbi-seg_0.0.20000620-7_i386.buildinfo 01388ccd3852c01a41d725ad5f9bda8d2dcc94e3a5457a9d44ed806bc28c7ba5 84464 ncbi-seg_0.0.20000620-7_i386.deb Files: c3d77fe32b9aec0043ff3c1b8cd5c489 26600 debug optional ncbi-seg-dbgsym_0.0.20000620-7_i386.deb ad6e253e6d549ff99204f2fe0dcd8341 4951 science optional ncbi-seg_0.0.20000620-7_i386.buildinfo 0778e515eaa978b733707b2641cf6c9b 84464 science optional ncbi-seg_0.0.20000620-7_i386.deb Thu Nov 21 02:21:32 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_14-51515.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/ncbi-seg_0.0.20000620-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/ncbi-seg_0.0.20000620-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/ncbi-seg_0.0.20000620-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/b1/ncbi-seg_0.0.20000620-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.oG27dbm4/b2/ncbi-seg_0.0.20000620-7_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.340s) 0.340s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 633ms CPU time consumed: 633ms Thu Nov 21 02:21:33 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 02:21:33 UTC 2024 I: ncbi-seg from trixie built successfully and reproducibly on i386. Thu Nov 21 02:21:35 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 02:21:35 UTC 2024 I: Submitting 8.0K b1/ncbi-seg_0.0.20000620-7_i386.buildinfo.asc Thu Nov 21 02:21:36 UTC 2024 I: Submitting 8.0K b2/ncbi-seg_0.0.20000620-7_i386.buildinfo.asc Thu Nov 21 02:21:37 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 02:21:37 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 02:21:37 UTC 2024 I: Removing signed ncbi-seg_0.0.20000620-7_i386.buildinfo.asc files: removed './b1/ncbi-seg_0.0.20000620-7_i386.buildinfo.asc' removed './b2/ncbi-seg_0.0.20000620-7_i386.buildinfo.asc'